Probing possible left- and right-handed poly(dinucleotide) helical conformations from (n–h) plots. models for polysequential nucleotides

Introducing the concept of the “dinucleotide” as the helical repeat, theoretical attempts have been made to determine possible single and double stranded helical structures by using helical parameter calculations and model building investigations. By virtue of its flexible framework, the dinucleotide repeat offers a much greater scope of finding new secondary structural forms for nucleic acids. Considering only those conformations which show tendency for at least partial base overlap as does the dinucleotide helical repeat, it has been possible to predict poly(dinucleotide) helical models in which successive phosphodiesters as well as nucleotide conformations alternate. More important, the recently found left-handed Z-type polynucleotide helix is characterized rather uniquely on the helical parameter plot. The results further suggest the possibility of other Z-type helices obtainable by alternative conformations for the exocyclic C4'–C5' bond and sugar pucker. Near neighbor long range conformational correlations between the dinucleotide repeat and the phosphodiester linking them have been established similar to poly(mononucleotide) helices. Need for considering higher repeats such as trinucleotide has been suggested to obtain models for looped out helical conformations.     

Structure and properties of the mesophase of syndiotactic polystyrene. I. Effect of casting conditions on the preparation of the mesophase

A syndiotactic polystyrene–toluene solution was cast under two different casting conditions to obtain the δ form. A systematic study of its conformational transition, thermal behavior, and structural transformation as functions of the annealing temperature and time was performed. Spectroscopic studies revealed the content of its helical conformations and its retention up to 190 °C. Thermal analyses showed a significant difference in the transformation from the γ form to the α form. The retention of the intermediate emptied clathrate form (mesophase) of the conformational order for a longer duration (from 120 to 180 °C) in a syndiotactic polystyrene membrane cast at room temperature was confirmed by X‐ray diffraction analysis. On the basis of the experimental results in this work, the transition mechanism is discussed. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 530–536, 2002; DOI 10.1002/polb.10120     

Conformational study of halogen- and hydrogen-substituted polythionylphosphazenes using density functional theory method

The structure and conformational stability of polythionylphosphazenes is investigated by modeling single polymer chains with small mimics. The model compounds are composed of repeat units of the corresponding polythionylphosphazenes. Two of the model compounds have hydrogens and two have chlorines as substituents on phosphorus atoms. The substituents on sulfur may be either fluorine or chlorine. Fully geometry-optimized structures and energies of the stable conformations involving rotations around the P? N bond near the sulfur are obtained using the density functional theory method. The structural and conformational analyses indicate that the rotation around the N? P bond leads to variations in the bond lengths, the SNP bond angle openings, as well as couplings between dihedral angles in different conformations in all model compounds. In addition, the conformational analysis suggests that the minima on the conformational potential energy surface in these compounds may be located in the vicinity of the following values of the NP? NS dihedral angle: -50°, 90° (or 60°), 180°, and 240°. It was found that the values of the conformational energy differences range between less than 1 to 5 kcal/mol. A comparison is made between the structural results obtained using the density functional theory and the ab initio molecular orbital theory for the global minimum structures. © 1995 John Wiley & Sons, Inc.     

Ab initio studies of structural features not easily amenable to experiment. 38. Structural and conformational investigations of propanoic, 2-methylpropanoic,and butanoic acid

The structures and conformational energies of several conformations of propanoic acid, 2-methylpropanoic acid, and butanoic acid were determined by geometrically unconstrained ab initio gradient geometry refinement on the 4-21G level. The O?C? C? C torsional potentials of propanoic acid and butanoic acid are found to be practically identical. There are energy minima at 0° and 120°, and maxima in the 60° region and at 180°. In 2-methylpropanoic acid there are energy minima at H? C? C?O dihedral angles of 0° and 120°, and maxima at 60° and 180°. The exact positions of the maxima and minima of the H? C? C?O torsional potential of 2-methylpropanoic acid are found to be predictable from propanoic acid rotational-potential parameters. Some conformationally dependent, local geometry trends are discussed.     

Calculation of structural behavior of indirect NMR spin-spin couplings in the backbone of nucleic acids

Calculated indirect NMR spin-spin coupling constants (J-couplings) between (31)P, (13)C, and (1)H nuclei were related to the backbone torsion angles of nucleic acids (NAs), and it was shown that J-couplings can facilitate accurate and reliable structural interpretation of NMR measurements and help to discriminate between their distinct conformational classes. A proposed stepwise procedure suggests assignment of the J-couplings to torsion angles from the sugar part to the phosphodiester link. Some J-couplings show multidimensional dependence on torsion angles, the most prominent of which is the effect of the sugar pucker. J-couplings were calculated in 16 distinct nucleic acid conformations, two principal double-helical DNAs, B- and A-, the main RNA form, A-RNA, as well as in 13 other RNA conformations. High-level quantum mechanics calculations used a baseless dinucleoside phosphate as a molecular model, and the effect of solvent was included. The predicted J-couplings correlate reliably with available experimental data from the literature.     

Ab initio studies of structural features not easily amenable to experiment. 25. Conformational analysis of methyl propanoate and comparison with the methyl ester of glycine

The molecular geometries of three conformations of methyl propanoate (MEP) (C? C? C?O torsions of 0°, 120°, and 180°) and the potential-energy surfaces of MEP (C? C? C?O torsions) and of the methyl ester of glycine (MEG) (N? C? C?O torsions) have been determined by ab initio gradient calculations at the 4-21G level. MEP has conformational energy minima at 0° and 120° of the C? C? C?O torsion, while the 60–90° range and 180° are energy maxima. For MEG there are two minima (at 0° and 180°) and one barrier to N? C? C?O rotation in the 60–90° range. The N? C? C?O barrier height is about twice as high (4 kcal/mol) as the C? C? C?O barrier. The 180° N? C? C?O minimum is characteristically wide and flat allowing for considerable flexibility of the N? C? C?O torsion in the 150–210° range. This flexibility could be of potential importance for polypeptide systems, since the N? C? C?O angles of helical forms are usually found in this region. The molecular structures of the methyl ester group CH₃OC(?O)CHRR′ in several systems are compared and found to be rather constant when R ? H and R′ ? H, CH₃, CH₃CH₂; or when R ? NH₂ and R′ ? H, CH₃, or CH(CH₃)₂.     

Physical properties and structure of silk. VI. Conformational changes in silk fibroin induced by immersion in water at 2 to 130°c

Silk fibroin films in the random-coil and β-form conformations were immersed in water at temperatures from 2 to 130°C, and conformational changes were followed by x-ray diffraction, infrared spectroscopy and differential scanning calorimetry. On treatment with water below 60°C, the random-coil conformation is converted to the α form and above 70°C to mixtures of the α and β conformations. The β-form content increases as the immersion temperature is raised. The β form is not affected by immersion in water in the temperature range studied.     

Ab initio studies of structural features not easily amenable to experiment. 30. Conformational analysis and molecular structures of propanal and butanal

The geometries of several conformations of propanal and butanal have been refined by geometrically unconstrained ab initio gradient relaxation on the 4-21G level. Both compounds possess energy minima at O? C? C? C torsional angles of 0° and in the 120° region, and energy maxima in the 70° region and at 180°. The structure of the aldehyde functional group is found to be relatively invariant both when different systems or when different conformations of the same system are compared. Conformationally dependent geometrical trends in propanal and butanal are discussed and found to be subtle yet noticeable.     

A dipole moment study of the conformational properties of diaryl diselenides and related compounds

The electric dipole moments of the diaryl diselenides (RC₆H₄)₂Se₂ (R  H, 4-F, 4-Br, 4-CH₃, 3-F) were measured in benzene solution at 25 and 45°C. The conformations of these compounds were deduced by matching experimental moments with values calculated for a variety of possible conformations. In the dissolved state the diselenides exist at 25°C in fixed “skew” conformations characterized by dihedral angles of 75–106° between the CSeSe planes, corresponding to the conformational energy minima. At 45°C oscillations about the SeSe bonds are excited in the diphenyl and bis(4-methylphenyl) diselenides, whereas the 4-bromophenyl derivative exhibits free rotation. The fluoro compounds have temperature-independent dipole moments, suggesting “rigid conformations” with dihedral angles of 106° (4-F) and 74.4° (3-F). An analysis of the dipole moments at 25 and 45°C obtained for the compounds (RC₆H₄)₂X₂ (R  H, 3-F, 4-F, 4-Br, 4-CH₃; X  S, Se, Te) showed that the conformational properties of these derivatives change on passing from X  S to X  Te. The observed variations are explicable in terms of a decreasing repulsion between the lone electron pairs of the chalcogen atoms on going from the disulfides to the ditellurides and a concomitant reduction of the energy barrier to rotations about the XX bonds.     

The Distinct Conformational Landscapes of 4S-Substituted Prolines That Promote an endo Ring Pucker

4-Substitution on proline directly impacts protein main chain conformational preferences. The structural effects of N-acyl substitution and of 4-substitution were examined by NMR spectroscopy and X-ray crystallography on minimal molecules with a proline 4S-nitrobenzoate. The effects of N-acyl substitution on conformation were attenuated in the 4S-nitrobenzoate context, due to the minimal role of the n→π* interaction in stabilizing extended conformations. By X-ray crystallography, an extended conformation was observed for most molecules. The formyl derivative adopted a δ conformation that is observed at the i+2 position of β-turns. Computational analysis indicated that the structures observed crystallographically represent the inherent conformational preferences of 4S-substituted prolines with electron-withdrawing 4-position substituents. The divergent conformational preferences of 4R- and 4S-substituted prolines suggest their wider structure-specific application in molecular design. In particular, the proline endo ring pucker favored by 4S-substituted prolines uniquely promotes the δ conformation [(ϕ, ψ) ≈(−80°, 0°)] found in β-turns. In contrast to other acyl capping groups, the pivaloyl group strongly promoted trans amide bond and polyproline II helix conformation, with a close n→π* interaction in the crystalline state, despite the endo ring pucker, suggesting its special capabilities in promoting compact conformations in ϕ due to its strongly electron-donating character.     

Enhanced sampling method in molecular simulations using genetic algorithm for biomolecular systems

We propose a molecular simulation method using genetic algorithm (GA) for biomolecular systems to obtain ensemble averages efficiently. In this method, we incorporate the genetic crossover, which is one of the operations of GA, to any simulation method such as conventional molecular dynamics (MD), Monte Carlo, and other simulation methods. The genetic crossover proposes candidate conformations by exchanging parts of conformations of a target molecule between a pair of conformations during the simulation. If the candidate conformations are accepted, the simulation resumes from the accepted ones. While conventional simulations are based on local update of conformations, the genetic crossover introduces global update of conformations. As an example of the present approach, we incorporated genetic crossover to MD simulations. We tested the validity of the method by calculating ensemble averages and the sampling efficiency by using two kinds of peptides, ALA3 and (AAQAA)₃. The results show that for ALA3 system, the distribution probabilities of backbone dihedral angles are in good agreement with those of the conventional MD and replica-exchange MD simulations. In the case of (AAQAA)₃ system, our method showed lower structural correlation of α-helix structures than the other two methods and more flexibility in the backbone ψ angles than the conventional MD simulation. These results suggest that our method gives more efficient conformational sampling than conventional simulation methods based on local update of conformations. © 2018 Wiley Periodicals, Inc.     

Structure Features of 1,3,5-Tris(Diphenylphosphinoxidemethylene)Ben zene in Crystal and Solution on the Base of X-Ray,Dipole Moments and Quantum Chemical Analysis

Abstract

The molecular structure, polarity and conformations in solution of 1,3,5-tris(diphenylphosphinoxidemethy1ene)benzene 1,3,5-[Ph₂P(0)CH₂]₃C₆H₃ have been studied by X-ray, dipole moments and quantum chemistry methods. It have been shown, that in crystal molecule has the conformation in which two diphenylphosphinoxide fragments dispose on one and the same side, but the third - on the other side of central benzene ring plane with torsion angles C_SP2-C_SP2-C_SP3-P 60–80° and C_SP2-C_SP3-P=O about 50–70°. In solution conformational picture is more rich: side by side with the structures realized in crystal, conformations with all three diphenylphosphinoxide fragments disposed on one and the same side of central benzene ring plane with torsion angles C_SP2-C_SP2-C_SP3-P 70-90° and C_SP2-C_SP3-P=O about 70–75° become preferable.     

2′‐De­oxy‐5‐propynyl­cytidine: a nucleoside forming two solid‐state conformations

The title compound, 4‐amino‐1‐(2‐deoxy‐β‐d ‐erythropentofuranosyl)‐5‐(prop‐1‐ynyl)pyrimidin‐2(1H)‐one, C₁₂H₁₅N₃O₄, shows two conformations in the crystalline state which differ mainly in the glycosylic bond torsion angle and the sugar pucker. Both mol­ecules exhibit an anti glycosylic bond conformation, with torsion angles χ = −135.0 (2) and −156.4 (2)° for mol­ecules 1 and 2, respectively. The sugar moieties show a twisted C2′‐endo sugar pucker (S‐type), with P = 173.3 and 192.5° for mol­ecules 1 and 2, respectively. The crystal structure is characterized by a three‐dimensional network that is stabilized by several inter­molecular hydrogen bonds between the two conformers.     

Ab initio studies of structural features not easily amenable to experiment: Part V. Conformational analysis of keto- and enol-acetone

The structures of several conformations of keto- and enol-acetone were determined by unconstrained ab initio geometry refinements using the 4-21G basis set. The geometry of propene was also refined to compare it with enol-acetone. The structural consequences of hyperconjugation for the local geometries of the methyl groups were determined in all conformations. In the most stable form of keto-acetone, one hydrogen atom of each methyl group was found in an eclipsed arrangement with respect to the carbonyl group. The stability of this crowded structure has previously been rationalized in terms of aromatic π-electron delocalization. This result is in contrast to one of two previous gas electron diffraction studies. It is concluded that the electron diffraction data may not contain enough information to determine the exact conformational arrangement of the methyl groups in acetone. The calculated structures are found to be in excellent agreement with experiment. Uncertainties in calculated bond distances and bond angles are on the order of magnitude of 0.01–0.02 Å and 1–2°, respectively.     

The application of molecular mechanics to the structures of carbohydrates

A study is reported of the accuracy with which the geometries of pyranose and methyl pyranoside molecules are predicted by molecular mechanics. Calculations of the conformational energies of the model compounds dihydroxymethane, methoxymethanol, and dimethoxymethane, made with the program MMI, produced results that compare well with previous ab initio molecular orbital calculations. This indicates that MMI gives a satisfactory account of the energetic and conformational aspects of the anomeric effect, a conclusion further supported by calculations on 2-methoxytetrahydropyran. The prediction of the observed preferred conformations of the primary alcohol group in aldohexopyranoses appears to be less satisfactory. MMI-CARB, a version of MMI with changes in some of the equilibrium C? O bond lengths of the program, has been used to calculate the geometries of 13 pyranose and methyl pyranoside molecules, the crystal structures of which have been studied by neutron diffraction. When the C? C? O? H torsion angles are constrained to approximately the values observed in the crystal structures, good agreement is obtained between the theoretical and experimental molecular geometries. The rms deviation for C? C and C? O bonds, excluding those significantly affected by thermal motion in the crystal structure determinations, is 0.005 Å. Corresponding figures for the valence angles that do not involve hydrogen atoms and for the ring torsion angles are 1.2° and 2.0°, respectively. The Cremer and Pople puckering parameters for the pyranose rings are reproduced within 0.026 Å in Q and 5.4° in θ.     

Ab initio studies of structural features not easily amenable to experiment. 18. Conformational analysis and molecular structure of glycine methyl ester

The structures of four conformations of the methyl ester of glycine were determined by standard single-determinant molecular orbital (MO ) calculations using Pulay's force method and the 4-21G basis set. The most stable conformation of this compound has a symmetry plane which contains all the heavy atoms; it is stabilized by hydrogen bonds between the NH₂ group and the carbonyl oxygen; it corresponds to the most stable, stretched form of free glycine. The structural parameters in the different conformations can vary significantly (bond distance by more than 0.02 Å and bond angles by up to 15°). The structural changes which are caused in glycine by esterification are discussed and some of them are interpreted in terms of hyperconjugative π-electron delocalization.     

Conformational memories with variable bond angles

Conformational Memories (CM) is a simulated annealing/Monte Carlo method that explores peptide and protein dihedral conformational space completely and efficiently, independent of the original conformation. Here we extend the CM method to include the variation of a randomly chosen bond angle, in addition to the standard variation of two or three randomly chosen dihedral angles, in each Monte Carlo trial of the CM exploratory and biased phases. We test the hypothesis that the inclusion of variable bond angles in CM leads to an improved sampling of conformational space. We compare the results with variable bond angles to CM with no bond angle variation for the following systems: (1) the pentapeptide Met-enkephalin, which is a standard test case for conformational search methods; (2) the proline ring pucker in a 17mer model peptide, (Ala)(8)Pro(Ala)(8); and (3) the conformations of the Ser 7.39 chi(1) in transmembrane helix 7 (TMH7) of the cannabinoid CB1 receptor, a 25-residue system. In each case, analysis of the CM results shows that the inclusion of variable bond angles results in sampling of regions of conformational space that are inaccessible to CM calculations with only variable dihedral angles, and/or a shift in conformational populations from those calculated when variable bond angles are not included. The incorporation of variable bond angles leads to an improved sampling of conformational space without loss of efficiency. Our examples show that this improved sampling leads to better exploration of biologically relevant conformations that have been experimentally validated.     

Conformational analysis of highly extended poly(ethylene terephthalate) chains by Monte Carlo calculations

The conformational disorder compatible with the highly extended chains found in mesomorphic poly(ethylene terephthalate) has been studied by Monte Carlo calculations on model oligomers confined inside cylindrical tubes. The distribution of torsional angles for such extended chains is characterized by O C C O bonds being always in the trans domain, while the C O C C bonds show an approximately similar probability of being found in trans and gauche states, the probability maxima being centered at 90° and −90° in the latter cases. At variance with the torsional angles of the O C C O and the ester bonds, always very close to 180°, the distributions for all other torsional angles show flat and broad probability maxima, indicating the possibility of substantial deviations from the average value inside each domain. This is also true for the fictitious O C˙˙˙C O bonds across the phenylene rings, for which a nearly trans geometry is preferred in extended conformations.     

Conformations of cyclobutane

The literature concerning the structures of compounds containing saturated, 4-carbon rings is reviewed critically, and the variety of conformations (dihedral angles of 0° to 30° ± 6°) of the cyclobutane ring are tabulated and discussed.